Genome Annotation Research Articles

The genome sequence of common vervain, Verbena officinalis L. (Verbenaceae)

We present a genome assembly of a specimen of common vervain, Verbena officinalis (Streptophyta; Magnoliopsida; Lamiales; Verbenaceae). The genome sequence has a total length of 289.20 megabases. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 495.81 kilobases and 153.46 kilobases, respectively. Gene annotation of this assembly on Ensembl identified 25,194 protein-coding genes.

Long-read transcriptomics of Ostreid herpesvirus 1 uncovers a conserved expression strategy for the capsid maturation module and pinpoints a mechanism for evasion of the ADAR-based antiviral defence

Abstract Ostreid herpesvirus 1 (OsHV-1), a member of the family Malacoherpesviridae (order Herpesvirales), is a major pathogen of bivalves. However, the molecular details of the malacoherpesvirus infection cycle and its overall similarity to the replication of mammalian herpesviruses (family Orthoherpesviridae) remain obscure. Here, to gain insights into the OsHV-1 biology, we performed long read sequencing of infected blood clams, Anadara broughtonii, which yielded over one million OsHV-1 long reads. This data enabled the annotation of the viral genome with 78 gene units and 274 transcripts, of which 67 were polycistronic mRNAs, 35 ncRNAs and 20 natural antisense transcripts (NATs). Transcriptomics and proteomics data indicate preferential transcription and independent translation of the capsid scaffold protein as an OsHV-1 capsid maturation protease isoform. The conservation of this transcriptional architecture across Herpesvirales likely indicates its functional importance and ancient origin. Moreover, we traced RNA editing events using short read sequencing and supported the presence of inosine nucleotides in native OsHV-1 RNA, consistent with the activity of ADAR1. Our data suggests that, whereas RNA hyper-editing is concentrated in specific regions of the OsHV-1 genome, single nucleotide editing is more dispersed along the OsHV-1 transcripts. In conclusion, we reveal the existence of a conserved pan-Herpesvirales transcriptomic architecture of the capsid maturation module and uncover a transcription-based viral counter defence mechanism, which presumably facilitates the evasion of the host ADAR antiviral system.

Transcription factor ASCL1 targets SLC6A13 to inhibit the progression of hepatocellular carcinoma via the glycine-inflammasome signaling.

Hepatocellular carcinoma (HCC), the most common primary liver cancer, typically arises from chronic liver conditions such as hepatitis, cirrhosis, or other chronic liver diseases, and is characterized by its aggressive nature and poor prognosis. The purpose of this research was to clarify the function of achaete-scute family bHLH transcription factor 1 (ASCL1) and solute carrier family 6 member 13 (SLC6A13) in influencing tumor cell behavior, inflammatory responses, and the regulation of inflammasomes. We analyzed the differentially expressed genes (DEGs) in the Cancer Genome Atlas-Liver Hepatocellular Carcinoma (TCGA-LIHC) database, as well as in the GSE14520 and GSE67764 datasets, to identify the expression changes of SLC6A13 in liver cancer. The prognostic significance of SLC6A13 in LIHC was assessed through Kaplan-Meier survival curve analysis. Transcriptional regulation of SLC6A13 by ASCL1 was explored using the Joint Annotation of the Human Genome and other species by the Systematic Pipeline for the Annotation of Regulatory Regions (JASPAR) database and dual-luciferase assays. In vitro experiments investigated the impact of ASCL1 and SLC6A13 overexpression on HCC cell growth. Additionally, the effects of ethanol treatment and glycine modulation on the inflammatory response in HCC cell lines were evaluated. HCC samples showed reduced levels of SLC6A13, which correlates with a better prognosis for liver metastases. Elevated SLC6A13 expression correlated with improved overall survival (OS), progression-free survival (PFS), recurrence-free survival (RFS), and disease-specific survival (DSS). ASCL1 upregulated SLC6A13 and inhibited proliferation, migration, and invasion of HCC cells. Ethanol induced the production of inflammatory cytokines, which was enhanced by overexpression of SLC6A13 but counteracted by glycine. This study highlighted elevated expression of SLC6A13 in LIHC which has been correlated with improved OS, PFS, RFS, and DSS. Overexpression of SLC6A13 and ASCL1 in HCC cells enhanced inflammasome activation, which was exacerbated by ethanol and attenuated by glycine.

Transcriptomic Analysis During Olive Fruit Development and Expression Profiling of Fatty Acid Desaturase Genes.

The olive fruit is a drupe whose development and ripening takes several months from flowering to full maturation. During this period, several biochemical and physiological changes occur that affect the skin color, texture, composition, and size of the mesocarp. The final result is a fruit rich in fatty acids, phenolic compounds, tocopherols, pigments, sterols, terpenoids, and other compounds of nutritional interest. In this work, a transcriptomic analysis was performed using flowers (T0) and mesocarp tissue at seven different stages during olive fruit development and ripening (T1-T7) of the 'Picual' cultivar. A total of 1755 genes overexpressed at any time with respect to the flowering stage were further analyzed. These genes were grouped into eight clusters based on their expression profile. The gene enrichment analysis revealed the most relevant biological process of every cluster. Highlighting the important role of hormones at very early stages of fruit development (T1, Cluster 1), whereas genes involved in fatty acid biosynthesis were relevant throughout the fruit developmental process. Hence, genes coding for different fatty acid desaturase (SAD, FAD2, FAD3, FAD4, FAD5, FAD6, and FAD7) enzymes received special attention. In particular, 26 genes coding for different fatty acid desaturase enzymes were identified in the 'Picual' genome, contributing to the improvement of the genome annotation. The expression pattern of these genes during fruit development corroborated their role in determining fatty acid composition.

The genome sequence of the willow leaf beetle, Lochmaea capreae Linnaeus, 1758.

We present a genome assembly from an individual female Lochmaea capreae (the willow leaf beetle; Arthropoda; Insecta; Coleoptera; Chrysomelidae). The genome sequence is 534.7 megabases in span. Most of the assembly is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.85 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,254 protein coding genes.

The genome sequence of pellitory-of-the-wall, Parietaria judaica L. (Urticaceae)

We present a genome assembly from an individual Parietaria judaica (pellitory-of-the-wall; Tracheophyta; Magnoliopsida; Rosales; Urticaceae). The genome sequence is 538.7 megabases in span. Most of the assembly is scaffolded into 13 chromosomal pseudomolecules. The three mitochondrial genomes have lengths of 215.28, 107.63 and 112.60 kilobases, while the plastid genome assembly had a length of 152.63 kilobases. Gene annotation of this assembly on Ensembl identified 35,329 protein-coding genes.

The genome sequence of the common awl robberfly, Neoitamus cyanurus (Loew, 1849).

We present a genome assembly from an individual female Neoitamus cyanurus (the common awl robberfly; Arthropoda; Insecta; Diptera; Asilidae). The genome sequence has a total length of 365.5 megabases. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.63 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,046 protein-coding genes.

The genome sequence of the Plain Wave moth, Idaea straminata (Borkhausen, 1794)

We present a genome assembly from an individual male Idaea straminata (the Plain Wave; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence spans 411.30 megabases. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 17.15 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,493 protein-coding genes.

Proteome-scale structural prediction of the giant Marseillevirus reveals conserved folds and putative homologs of the hypothetical proteins.

A significant proportion of the highly divergent and novel proteins of giant viruses are termed "hypothetical" due to the absence of detectable homologous sequences in the existing databases. The quality of genome and proteome annotations often relies on the identification of signature sequences and motifs in order to assign putative functions to the gene products. These annotations serve as the first set of information for researchers to develop workable hypotheses for further experimental research. The structure-function relationship of proteins suggests that proteins with similar functions may also exhibit similar folding patterns. Here, we report the first proteome-wide structure prediction of the giant Marseillevirus. We use AlphaFold-predicted structures and their comparative analysis with the experimental structures in the PDB database to preliminarily annotate the viral proteins. Our work highlights the conservation of structural folds in proteins with highly divergent sequences and reveals potentially paralogous relationships among them. We also provide evidence for gene duplication and fusion as contributing factors to giant viral genome expansion and evolution. With the easily accessible AlphaFold and other advanced bioinformatics tools for high-confidence de novo structure prediction, we propose a combined sequence and predicted-structure-based proteome annotation approach for the initial characterization of novel and complex organisms or viruses.

The genome sequence of a fold-wing cranefly, Ptychoptera albimana (Fabricius, 1787)

We present a genome assembly from an individual male fold-wing cranefly, Ptychoptera albimana (Arthropoda; Insecta; Diptera; Ptychopteridae). The genome sequence has a total length of 197.90 megabases. Most of the assembly (97.54%) is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 18.05 kilobases in length. Gene annotation of this assembly on Ensembl identified 10,210 protein-coding genes.

TE-Seq: A Transposable Element Annotation and RNA-Seq Pipeline.

The recognition that transposable elements (TEs) play important roles in many biological processes has elicited growing interest in analyzing sequencing data derived from this 'dark genome'. This is however complicated by the highly repetitive nature of these sequences in genomes, requiring the deployment of several problem-specific tools as well as the curation of appropriate genome annotations. This pipeline aims to make the analysis of TE sequences and their expression more generally accessible. The TE-Seq pipeline conducts an end-to-end analysis of RNA sequencing data, examining both genes and TEs. It implements the most current computational methods tailor- made for TEs, and produces a comprehensive analysis of TE expression at both the level of the individual element and at the TE clade level. Furthermore, if supplied with long-read DNA sequencing data, it is able to assess TE expression from non-reference (polymorphic) loci. As a demonstration, we analyzed proliferating, early senescent, and late senescent lung fibroblast RNA-Seq data, and created a custom reference genome and annotations for this cell strain using Nanopore sequencing data. We found that several retrotransposable element (RTE) clades were upregulated in senescence, which included non-reference, intact, and potentially active elements. TE-Seq is made available as a Snakemake pipeline which can be obtained at https://github.com/maxfieldk/TE-Seq . All software dependencies besides Snakemake and Docker/Singularity are packaged into a container which is automatically built and deployed by the pipeline at runtime.

The Highly Repetitive Genome of Myxobolus rasmusseni, an Emerging Myxozoan Parasite of Fathead Minnows.

Myxozoans are a monophyletic taxon of approximately 2,400 described species of parasites from the phylum Cnidaria. The recent focus on their negative impacts on fisheries, on their evolution from free-living ancestors, and on their emergence into new fish host populations has stressed the critical need for genomic resources for this parasitic group. Here, we describe the genome assembly and annotation of Myxobolus rasmusseni, an emerging parasite of fathead minnows in Alberta, Canada. The assembly is 174.6 Mb in size, 68% of which is made up of repetitive elements, making it one of the most repetitive animal genomes sequenced to date. Through comparisons to other myxozoans, we show that widespread gene loss, a known phenomenon of this group of parasites, is consistent with closely related species. Additionally, we assembled the M. rasmusseni mitochondrial genome, which is nearly twice the size of the typical animal mitochondrial genome yet contains only five of the canonical mitochondrial protein-coding genes and open reading frames not found in other myxozoans. These results add to our understanding of the gene- and genome-level diversity observed in myxozoans.

Quest for Orthologs in the Era of Biodiversity Genomics.

The era of biodiversity genomics is characterised by large-scale genome sequencing efforts that aim to represent each living taxon with an assembled genome. Generating knowledge from this wealth of data has not kept up with this pace. We here discuss major challenges to integrating these novel genomes into a comprehensive functional and evolutionary network spanning the tree of life. In summary, the expanding datasets create a need for scalable gene annotation methods. To trace gene function across species, new methods must seek to increase the resolution of ortholog analyses, e.g., by extending analyses to the protein domain level and by accounting for alternative splicing. Additionally, the scope of orthology prediction should be pushed beyond well-investigated proteomes. This demands the development of specialised methods for the identification of orthologs to short proteins and non-coding RNAs, and for the functional characterization of novel gene families. Furthermore, protein structures predicted by machine learning are now readily available, but this new information is yet to be integrated with orthology-based analyses. Finally, an increasing focus should be placed on making orthology assignments adhere to the FAIR principles. This fosters green bioinformatics by avoiding redundant computations and helps integrating diverse scientific communities sharing the need for comparative genetics and genomics information. It should also help with communicating orthology-related concepts in a format that is accessible to the public, to counteract existing misinformation about evolution.

The genome sequence of the corn cockle, Agrostemma githago L., 1753 (Caryophyllaceae)

We present a genome assembly from an individual Agrostemma githago (the corn cockle; Tracheophyta; Magnoliopsida; Caryophyllales; Caryophyllaceae). The genome sequence has a total length of 1,735.0 megabases. Most of the assembly is scaffolded into 24 chromosomal pseudomolecules suggesting the individual is a tetraploid (2n = 4x = 48). The organelle genomes have been assembled, and the length of the mitochondrial genome is 262.91 and the plastid genome 151.73 kilobases in length. Gene annotation of this assembly on Ensembl identified 38,816 protein-coding genes.

The genome sequence of a leaf beetle, Galeruca laticollis Sahlberg, C.R., 1838

We present a genome assembly from an individual leaf beetle, Galeruca laticollis (Arthropoda; Insecta; Coleoptera; Chrysomelidae). The genome sequence has a total length of 2,154.60 megabases. Most of the assembly (99.92%) is scaffolded into 12 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 19.98 kilobases in length. Gene annotation of this assembly on Ensembl identified 32,229 protein-coding genes.

The genome sequence of fat-hen, Chenopodium album L.

We present a genome assembly from an individual Chenopodium album (fat-hen; Streptophyta; Magnoliopsida; Caryophyllales; Chenopodiaceae). The genome sequence has a total length of 1,593.80 megabases. Most of the assembly (99.61%) is scaffolded into 27 chromosomal pseudomolecules suggesting the individual is an allohexaploid (2n = 6x = 54). The mitochondrial and plastid genome assemblies have lengths of 312.95 kilobases and 152.06 kilobases, respectively. Gene annotation of this assembly on Ensembl identified 50,077 protein-coding genes.

Marker trait association and candidate gene identification for brown rust disease in sugarcane

AbstractBrown rust (caused by Puccinia melanocephala H. & P. Sydow) is one of the most devastating diseases in commercial sugarcane production. It could reduce sugarcane yield by up to 50% depending on the susceptibility levels of cultivars. Breeding disease‐resistant cultivars is the most effective, economical, and environmentally friendly option to control brown rust. A genome‐wide association study was conducted on a field trial using 432 sugarcane clones following an augmented design with two replications. Brown rust was screened using the whorl inoculation method over two crop cycles. The genotype data were obtained through target enrichment sequencing technologies. The gene actions considering six different models and marker dosage effects were included during the marker‐trait analysis. A total of seven, nine, and seven nonredundant marker‐trait associations were identified for plant cane, first ratoon, and across two crop cycles, respectively. The most significant (p‐value 6.17E−20) marker (chr01p59833543) has the additive effect of −0.63 for the diplo‐additive model and reduced disease severity the most (41.35%) due to heterozygote (AG) over homozygote allele (AA) combination in the tested clones. Gene annotation of the monoploid sugarcane genome R570 suggested that six putative candidate genes were co‐located with significant markers associated with brown rust resistance in sugarcane. The putative candidate genes regulated the formation of a cell wall barrier that plays a crucial role in controlling brown rust pathogen infection. The results of this study will open the path to exploiting new resistance sources for brown rust resistance in commercial sugarcane.

The genome sequence of a soldier beetle, Cantharis flavilabris Fallén, 1807

We present a genome assembly from an individual female Cantharis flavilabris (soldier beetle; Arthropoda; Insecta; Coleoptera; Cantharidae). The genome sequence is 348.3 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,711 protein coding genes.

The genome sequence of a lauxaniid fly, Tricholauxania praeusta (Fallén, 1820)

We present a genome assembly from an individual female Tricholauxania praeusta (a lauxaniid fly; Arthropoda; Insecta; Diptera; Lauxaniidae). The genome sequence has a total length of 661.30 megabases. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.31 kilobases in length. Gene annotation of this assembly on Ensembl identified 25,606 protein-coding genes.

The genome sequence of the Vapourer moth, Orgyia antiqua (Linnaeus, 1758).

We present a genome assembly from an individual male Orgyia antiqua specimen (the Vapourer moth; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 480.1 megabases in span. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,475 protein coding genes.